
########
# Usage: Rscript detail_pathway_boxplot2.R 'P00001' "wilcox.test" "Healthy,HCC"

# 传入参数： target = 'P00001' 
#            testMethod = "wilcox.test"      # testMethod = "wilcox.test"   or   testMethod = "t.test" 
#            cohort.selected = c('Healthy', 'HCC')
########
library(ggplot2)
library(ggpubr)
library(RColorBrewer)

library(optparse)

option_list <- list(
  make_option("--t", default = "", type = "character", help = "target"),
  make_option("--i", default = "", type = "character", help = "target file"),
  make_option("--l", default = "", type = "character", help = "log"),
  make_option("--m", default = "", type = "character", help = "test method"),
  make_option("--c", default = "", type = "character", help = "cohort selected"),
  make_option("--o", default = "", type = "character", help = "output png file")
)
opt <- parse_args(OptionParser(option_list = option_list))

Args = commandArgs()
target = opt$t
testMethod = opt$m
cohort.selected =opt$c
cohort.selected = as.vector(unlist(strsplit(cohort.selected, ',')))

# target = 'P00101'
# testMethod = "wilcox.test"      # testMethod = "wilcox.test"   or   testMethod = "t.test"
# cohort.selected = c('Healthy', 'HCC')
# path = "D:\\exo\\905\\submit 10\\detail_pathway"
# setwd(path)

targetType = 'pathway'
w=6
h=6
outfile =opt$o

infile = opt$i
data.target = read.csv(infile, sep=',', header = FALSE, row.names = NULL,stringsAsFactors = F)
pathwayName = data.target[1, ][5]       ### 获取pathway name
data.target = data.target[-1, ]
colnames(data.target) = c('sample', 'type', 'cohort', 'sampleSize', 'score')
data.target = data.target[data.target$cohort %in% cohort.selected, ]
data.target$label = paste(data.target$cohort, '\n', '(', data.target$sampleSize,')', sep='')   ### label
data.target$score = round(as.numeric(data.target$score), 3)

cols = c(brewer.pal(9,"Pastel1"), brewer.pal(9,"Set3"))
pdf(outfile, width=w, height=h)
my_comparisons <- list(unique(data.target$label))
p = ggplot(data.target, aes(x = label, y = score, fill=label))+
  geom_boxplot(linetype = "dashed", width=0.6, outlier.shape = NA, color="#525252", size=0.5, notch = TRUE) +
  stat_boxplot(aes(ymin = ..lower.., ymax = ..upper..), width=0.6, outlier.shape = NA, color="#525252", size=0.5, notch = TRUE) +
  stat_boxplot(geom = "errorbar", aes(ymin = ..ymax..), color="#525252", size=0.5, width=0.3) +
  stat_boxplot(geom = "errorbar", aes(ymax = ..ymin..), color="#525252", size=0.5, width=0.3)+
  stat_compare_means(comparisons = my_comparisons, method=testMethod,label = "p.signif", vjust = 0.5)+
  scale_fill_manual(values = cols)+
  xlab('')+ylab("ssGSEA score")+
  ggtitle(pathwayName)+
  theme_bw() + theme(panel.grid = element_blank())+
  theme(axis.title = element_text(size = 12, face = "bold"))+
  theme(plot.title = element_text(size = 14, face = "bold", hjust = 0.5))+
  guides(fill = FALSE, colour = FALSE)+
  theme(panel.border = element_rect(linetype = 'solid', size = 1.2,fill = NA),
        axis.text.y = element_text(face = 'bold',color = 'black',size = 10, angle = 360),
        axis.text.x = element_text(face = 'bold',color = 'black',size = 10, angle = 360, hjust = 0.5),
        axis.title = element_text(size = 14, face = "bold"))
print(p)
dev.off()
